Bonneville and Windsor, who will be the first woman to tackle the role, will appear in the Monty Python musical via pre-recorded video segments, which usually feature Eric Idle, for one week at a time as part of the Summer of Charity Gods scheme.
Simon Callow, Larry Lamb, Christopher Biggins and Bradley Walsh will also be among stars playing God for good causes.
They will all donate their fee to a number of charities including the Make-A-Wish Foundation and Great Ormond Street children's hospital.
Bonneville, 49, who will be the first to appear in the show when his run starts on Monday (15Jul13), is joining the scheme in support of a London-based charity for young people, while he also has a personal connection to Spamalot as one of his relatives appeared in Monty Python and the Holy Grail, the 1975 comedy film on which the show is based.
He says, "I wanted to play God in Spamalot in order to support Scene & Heard, a north London charity, which (helps young people)... I'm also delighted to be involved with the show because an ancestor on my mother's side was in fact one of the knights who say 'Ni'."
Windsor adds, "I wanted to play God in Spamalot because having been four foot 10 and a half inches tall all my life, this would be the first and only time people would look up to me."
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